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shendurelab / LACHESIS

The LACHESIS software, as described in Nature Biotechnology (http://dx.doi.org/10.1038/nbt.2727)
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GenomeLinkMatrix error #20

Open okokookk opened 7 years ago

okokookk commented 7 years ago

Hi, I have one problem. When I run LACHESIS, I got this error. How can I do if I want to solve this problem?

N_clusters = 31, N_singletons = 6 Total length in singleton clusters = 31570 Total length of all clustered contigs = 2921503406 out of 2944539404 (99.2177%) Lachesis: GenomeLinkMatrix.cc:1133: void GenomeLinkMatrix::ValidateClusters(const TrueMapping*, bool) const: Assertion `( same_cluster ? N_links_same_cluster : N_links_diff_cluster ) >= 0' failed. Aborted

fbemm commented 7 years ago

Any ideas why this is happening?

okokookk commented 7 years ago

In my opinion, because the number is outside the capacity that int64 can accommodate. So you can modify the following file and re-compile.

1121 line in the GenomeLinkeMatrix.cc int64_t N_links_same_cluster = 0, N_links_diff_cluster = 0; '>' unsigned long long N_links_same_cluster = 0, N_links_diff_cluster = 0;

I'm not sure if this is correct. but, if you change this way, it will run without this problems.

fbemm commented 7 years ago

Works but I think its causing downstream issues. During ordering (Filling 9 clusters with Hi-C data from SAM file) no links are pulled out from the alignment files. Basically no dots show up and then also none of the contigs within a cluster are ordered. Anyone seen this before? Might be unrelated ...

ghuryejay commented 6 years ago

Did anyone figure this out?

yeswzc commented 6 years ago

I met same problem too. Is there a certain solution ?

Lordhooze commented 5 years ago

any solutions？

jazberna1 commented 4 years ago

Hi,

The solution mentioned above worked for me at least.

Jorge